Tag: protein

Newly identified protein could help fight cancer

Newly identified protein could help fight cancer

Researchers from the University of British Columbia (UBC) have identified a new protein that helps an oral bacterium thrive in other locations around the body. The discovery could eventually lead to the development of new drugs that specifically target the protein.

“This bacterium is common in the mouths of humans and generally doesn’t cause disease in that location. However, it can travel through the bloodstream to other areas of the body, which leads to some pretty big health concerns,” says Dr. Kirsten Wolthers, Associate Professor of Biochemistry and Microbiology at UBC’s Okanagan Campus.

Most notably, this bacteria is prevalent in the tumors of colorectal cancer patients. The presence of the bacteria can contribute to tumor growth, spread of cancer to other sites in the body, and resistance to chemotherapy.

With the help of the CMCF beamline at the Canadian Light Source (CLS), located at the University of Saskatchewan, Wolthers and her colleagues determined that the new protein they identified enables the bacteria to take essential nutrients, such as iron, from our blood cells.

Read more on the CLS website

Image: Alexis Gauvin, inspecting a protein sample for particulate matter, using the glove box. Gauvin is a biochemistry student and a member of Dr. Kirsten Wolthers’s research group in the Department of Chemistry, University of British Columbia (Okanagan Campus).

Picking up good vibrations – of proteins – at CHESS

Picking up good vibrations – of proteins – at CHESS

A new method for analyzing protein crystals – developed by Cornell researchers and given a funky two-part name – could open up applications for new drug discovery and other areas of biotechnology and biochemistry.

The development, outlined in a paper published March 3 in Nature Communications, provides researchers with the tools to interpret the once-discarded data from X-ray crystallography experiments – an essential method used to study the structures of proteins. This work, which builds on a study released in 2020, could lead to a better understanding of a protein’s movement, structure and overall function.

Protein crystallography produces bright spots, known as Bragg peaks, from the crystals, providing high-resolution information about the shape and structure of a protein. This process also captures blurry images – patterns and clouds related to the movement and vibrations of the proteins – hidden in the background of the Bragg peaks.

These background images are typically discarded, with priority given to the bright Bragg peak imagery that is more easily analyzed.

“We know that this pattern is related to the motion of the atoms of the protein, but we haven’t been able to use that information,” said lead author Steve Meisburger, Ph.D. ’14, a former postdoctoral researcher in the lab of Nozomi Ando, M.S. ’04, Ph.D. ’09, associate professor of chemistry and chemical biology in the College of Arts and Sciences. “The information is there, but we didn’t know how to use it.  Now we do.”

Meisburger worked closely with Ando to develop the robust workflow to decode the weak background signals from crystallography experiments called diffuse scattering. This allows researchers to analyze the total scattering from crystals, which depends on both the protein’s structure and the subtle blur of its movements.

Their two-part method – which the team dubbed GOODVIBES and DISCOBALL – simultaneously provides a high-resolution structure of the protein and information on its correlated atomic movements.

GOODVIBES analyzes the X-ray data by separating the movements – subtle vibrations – of the protein from other proteins that might be moving around it. DISCOBALL independently validates these movements for certain proteins directly from the data, allowing researchers to trust the results from GOODVIBES and understand what the protein might be doing.

Read more on CHESS website

Image: Meisburger, Case, & Ando (2020) Nat Commun 11, 1271

Sirius helps reveal previously unknown process of maturation for key protein in SARS-CoV-2 replication

Sirius helps reveal previously unknown process of maturation for key protein in SARS-CoV-2 replication

Researchers at USP in São Carlos combined cutting-edge technologies and demonstrated that a molecule targeted by medications behaves differently than previously theorized.

A group of researchers from the University of São Paulo in São Carlos has just presented their findings from research indicating a new understanding of the maturation process and how inhibitors act upon the Mpro protein, an essential component in the life cycle of the Sars-CoV-2 virus and the target of various efforts to develop medications to treat Covid-19. Their results appear in an article entitled “An in-solution snapshot of SARS-COV-2 main protease maturation process and inhibition,” published in the journal Nature Communications (https://doi.org/10.1038/s41467-023-37035-5).

Mpro is an abbreviation for main protease, because of its importance to the virus. Today, two medications are available which interact with this molecule to treat covid-19. Still, some of the processes in this protein’s activity are not yet entirely understood, and this was the object of the study undertaken at Sirius.

As part of the role it plays in the life cycle of the Sars-CoV-2 virus, Mpro undergoes a series of modifications until it reaches its final form. Part of this process had already been described by the group from São Carlos, directed by Professor Glaucius Oliva.

André Godoy, who led the group, was one of the first external users of Sirius, the cutting- synchrotron light source planned and built by the Brazilian Center for Research in Energy and Materials (CNPEM), an organization overseen by the Ministry of Science, Technology and Innovation (MCTI).

In September 2020 he brought approximately 200 crystals containing proteins from the Sars-CoV-2 virus for analysis in the Manacá beamline, which was developed for experiments involving X-ray diffraction crystallography. “The Manacá beamline was the first research station to open at Sirius, as the result of a task-force effort at the CNPEM to support research exploring molecular mechanisms related to covid-19. This is one of the publications that resulted from this effort,” explains Harry Westfahl, Director of the Brazilian Synchrotron Light National Laboratory (LNLS).

Read more on the LNLS website

Image: Cryomicroscopy map of the Mpro dimer interacting with the N-terminal. Image obtained from analyses conducted at Diamond and Sirius by the USP São Carlos group

How vision begins

How vision begins

Researchers at the Paul Scherrer Institute PSI have deciphered the molecular processes that first occur in the eye when light hits the retina. The processes – which take only a fraction of a trillionth of a second – are essential for human sight. The study has now been published in the scientific journal Nature.

It only involves a microscopic change of a protein in our retina, and this change occurs within an incredibly small time frame: it is the very first step in our light perception and ability to see. It is also the only light-dependent step. PSI researchers have established exactly what happens after the first trillionth of a second in the process of visual perception, with the help of the SwissFEL X-ray free-electron laser of the PSI.

At the heart of the action is our light receptor, the protein rhodopsin. In the human eye it is produced by sensory cells, the rod cells, which specialise in the perception of light. Fixed in the middle of the rhodopsin is a small kinked molecule: retinal, a derivative of vitamin A. When light hits the protein, retinal absorbs part of the energy. With lightning speed, it then changes its three-dimensional form so the switch in the eye is changed from “off” to “on”. This triggers a cascade of reactions whose overall effect is the perception of a flash of light.

Read more on the PSI website

Image: PSI researcher Valérie Panneels purifies the red protein rhodopsin in order to examine it later at the SwissFEL X-ray free-electron laser

Credit:  Scanderbeg Sauer Photography

Battling biofilm to prevent dangerous lung infections

Battling biofilm to prevent dangerous lung infections

Researchers from the University of Toronto (U of T) and The Hospital for Sick Children have identified a promising therapeutic target to help treat lung infections in cystic fibrosis (CF) patients.

“Individuals with cystic fibrosis have an impairment in their lungs where they have a hard time clearing out the mucus that accumulates within the lungs,” says Andreea Gheorghita, PhD candidate in the Department of Biochemistry at U of T.

Pseudomonas aeruginosa is a bacterium that causes opportunistic infections in individuals with weakened immune systems or other health concerns. For individuals with CF, repeated Pseudomonas infections often lead to long hospital stays and severe lung damage.

“Because of the impaired ability to clear mucus in the airways, these lung infections can become very persistent and prolonged, which eventually leads to lung tissue damage, loss of lung function, and eventually can cause patient mortality,” says Gheorghita.

Using the CMCF beamline at the Canadian Light Source (CLS) at the University of Saskatchewan (USask), the team has been able to visualize the interaction between two important proteins that are key players in Pseudomonas’s ability to make biofilm. This sticky secretion allows the bacterium to attach to the lungs and makes it difficult for antibiotics and the patient’s immune system to fight the infection.

Read more on the  Canadian Light Source website

Insights into coronavirus proteins using SAXS

Insights into coronavirus proteins using SAXS

A collaboration led by researchers from the European Molecular Biology Laboratory (EMBL) used small angle X-ray scattering (SAXS) at the European XFEL and obtained interesting data on samples containing coronavirus spike proteins including proteins of the isolated receptor biding domain. The results can, for example, help investigate how antibodies bind to the virus. This gives researchers a new tool that may improve understanding of our bodies’ immune response to coronavirus and help to develop medical strategies to overcome COVID-19

SAXS is a powerful technique as it allows researchers to gain insights into protein shape and function at the micro- and nanoscales. The technique has proven to be extremely useful in investigating macromolecular structures such as proteins, especially because it removes the need to crystallize these samples. This means researchers can study the sample in its native form under physiological conditions under which biological reactions occur.

Read more on the European XFEL website

Image: Seen here, the instrument SPB/SFX, where the SAXS experiment was carried out. Using this instrument researchers can study the three-dimensional structures of biological objects. Examples are biological molecules including crystals of macromolecules and macromolecular complexes as well as viruses, organelles, and cells.

Credit: European XFEL / Jan Hosan

Towards a therapy for Parkinson’s disease

Towards a therapy for Parkinson’s disease

Over 100,000 Canadians are living with Parkinson’s disease and 25 more are diagnosed every day, according to Parkinson Canada.

Patients experience tremors, stiffness, and difficulty with movement. Dr. Jean-Francois Trempe, an Associate Professor with McGill University, and colleagues are using the Canadian Light Source (CLS) at the University of Saskatchewan to help search for potential drug targets for the disease.

“I work on a set of proteins that are involved in quality control,” said Trempe. “These proteins are able to sort the damaged proteins from the non-damaged proteins and they send the damaged ones off to be degraded and that’s important for the long-term survival of neurons.”

His team used bright synchrotron light at the CLS to gain insights into a protein involved in formation of flagella, which are important notably for fluid circulation in the brain. By finding new information about this protein, their team is contributing to a body of knowledge that will hopefully lead to a therapy down the road.

Read more and watch the video on the CLS website

The egg in the X-ray beam

The egg in the X-ray beam

Innovative time-resolved method reveals network formation by and dynamics of proteins.

A team of scientists has been using DESY’s X-ray source PETRA III to analyse the structural changes that take place in an egg when you cook it. The work reveals how the proteins in the white of a chicken egg unfold and cross-link with each other to form a solid structure when heated. Their innovative method can be of interest to the food industry as well as to the broad field of research surrounding protein analysis. The cooperation of two groups, headed by Frank Schreiber from the University of Tübingen and Christian Gutt from the University of Siegen, with scientists at DESY and European XFEL, reports the research in two articles in the journal Physical Review Letters.

Eggs are among the most versatile food ingredients. They can take the form of a gel or a foam, they can be comparatively solid and also serve as the basis for emulsions. At about 80 degrees Celsius, egg white becomes solid and opaque. This is because the proteins in the egg white form a network structure. Studying the exact molecular structure of egg white calls for energetic radiation, such as X-rays which is able to penetrate the opaque egg white and has a wavelength that is not longer than the structures being examined.

Read more on the DESY website

Image: When heated, the proteins in the originally transparent chicken egg white form a tightly meshed, opaque network.

Credit: DESY, Gesine Born

Experimental drug targets HIV in a novel way

Experimental drug targets HIV in a novel way

SCIENTIFIC ACHIEVEMENT

Using the Advanced Light Source (ALS), researchers from Gilead Sciences Inc. solved the structure of an experimental HIV drug bound to a novel target: the capsid protein that forms a shield around the viral RNA.

SIGNIFICANCE AND IMPACT

The work could lead to a long-lasting treatment for HIV that overcomes the problem of drug resistance and avoids the need for burdensome daily pill-taking.

Progress in HIV treatment still needed

Over the past couple of decades, safe and effective treatment for HIV infection has turned what was once a death sentence into a chronic disease. Today, people on the latest HIV drugs have near-normal life expectancy.

However, many people are still living with multidrug-resistant HIV, unable to control their virus loads with currently available HIV drugs. The virus develops resistance when people take their pills inconsistently due to forgetfulness, side effects, or a complex schedule. To some, taking a pill every day is a burden: they schedule their lives around it for fear of missing a dose. To others, it is a stigma, as it makes it difficult to hide one’s HIV status from close friends and family.

Read more on the Advanced Light Source website

Image: An experimental small-molecule drug (GS-6207) targets the protein building blocks of the HIV capsid—a conical shell (colored red in this artistic rendering) that encloses and protects the viral RNA—making the virus unable to replicate in cells. Credit Advanced Light Source

How cellular proteins control cancer spread

How cellular proteins control cancer spread

New finding may help focus the search for anti-cancer drugs

A new insight into cell signals that control cancer growth and migration could help in the search for effective anti-cancer drugs. A team of researchers has revealed key biochemical processes that advance our understanding of colorectal cancer, the third most common cancer among Canadians.

Using the CMCF beamline at the Canadian Light Source (CLS) at the University of Saskatchewan, scientists from McGill University and Osaka University in Japan were able to unlock the behavior of an enzyme involved in the spread of cancer cells. The team found that there is a delicate interaction between the enzyme, PRL3, and another protein that moves magnesium in and out of cells. This interaction is crucial to colorectal cancer growth.

A new insight into cell signals that control cancer growth and migration could help in the search for effective anti-cancer drugs. A team of researchers has revealed key biochemical processes that advance our understanding of colorectal cancer, the third most common cancer among Canadians.

Using the CMCF beamline at the Canadian Light Source (CLS) at the University of Saskatchewan, scientists from McGill University and Osaka University in Japan were able to unlock the behavior of an enzyme involved in the spread of cancer cells. The team found that there is a delicate interaction between the enzyme, PRL3, and another protein that moves magnesium in and out of cells. This interaction is crucial to colorectal cancer growth.

Read more on the Canadian Light Source website

Image: Members of the Gehring research laboratory discussing the results of a protein purification.

Cross-β Structure – a Core Building Block for Streptococcus mutans Functional Amyloids

Cross-β Structure – a Core Building Block for Streptococcus mutans Functional Amyloids

Most amyloids1 are misfolded proteins, having enormous variety in native structures. Pathological amyloids are implicated in diseases including Alzheimer’s disease and many others.  They are characterized by long, unbranched fibrillar structure, enhanced birefringence on binding Congo red dye, and cross-β structure – β-strands running approximately perpendicular to the fibril axis, forming long β-sheets running in the direction of the axis.  Fiber diffraction patterns from amyloids are marked by strong intensity at about 4.8 Å in the meridional direction (parallel to the fibril axis), corresponding to the separation of strands in a β-sheet, and in many cases broader but distinct equatorial intensity at about 10 Å.  The 10 Å intensity (whose position may vary considerably) comes from the distance between stacked β-sheets.  This stacking is characteristic of the many amyloids formed by small peptides, including peptide fragments of larger amyloidogenic proteins.  While some authors have required the 10 Å intensity to characterize an amyloid, it is not strictly necessary, since architecturally more complex examples have been found of Congo-red-staining fibrils with cross-β structure, but without the stacked-sheet structure, and consequently without the 10 Å intensity on the equator.

Amyloids do not always stem from protein misfolding.  Organisms across all kingdoms utilize functional amyloids in numerous biological processes.  Bacteria are no exception. Bacterial amyloids contribute to biofilm formation and stability.  Tooth decay is the most common infectious disease in the world.  A major etiologic agent, Streptococcus mutans, is a quintessential biofilm dweller that produces at least three different amyloid-forming proteins, adhesins P1 and WapP, and the cell density and competence regulator Smu_63c2.  The naturally occurring truncation derivatives of P1 and WapA, C123 and AgA, represent the amyloidogenic moieties, and a new paradigm of Gram-positive bacterial adhesins is emerging of adhesins having dual functions in monomeric and amyloid forms. While each S. mutans protein possesses considerable β-sheet structure, the tertiary structures of each protein are quite different (Fig. 1).  This study further characterized S. mutans amyloids and addressed the ongoing debate regarding the underlying structure and assembly of bacterial amyloids including speculation that they are structurally dissimilar from better-characterized amyloids.

Read more on the SSRL website

Image: Crystal or predicted 3D structures of S. mutans C123 (left), AgA (center), and Smu_63c (right).

Unravelling the secrets of the malaria parasite

Unravelling the secrets of the malaria parasite

PETRA III helps to identify a new kind of protein in Plasmodium falciparum

For the first time, scientists have identified a lipocalin protein in the malaria parasite Plasmodium falciparum. The discovery helps to better understand the life cycle of the parasite that is a major health burden in large parts of the world. The cooperation between the groups of Tim Gilberger from the Centre for Structural Systems Biology CSSB (Cellular Parasitology Department at Bernhard Nocht Institute for Tropical Medicine/ Universität Hamburg) at DESY and Matthias Wilmanns from the Hamburg branch of the European Molecular Biology Laboratory EMBL describes the discovery in the journal Cell Reports. CSSB is a cooperation of nine institutions, including DESY, that have deputed scientists to the centre.

With an estimated 228 million cases per year worldwide and more than 400,000 deaths, malaria remains one of the most important human health threats. There is no vaccine commercially available. While biologists have revealed many details about how the malaria parasite rapidly feeds on and transforms its host’s red blood cells, there are many unsolved mysteries surrounding the parasite’s life cycle. Using the microscopic facilities available at CSSB in combination with EMBL’s X-ray beamlines at DESY’s research light source PETRA III, the team unraveled a small piece of this mystery with the identification and characterization of the first lipocalin in the most virulent malaria parasite species P. falciparum.

Read more on the PETRA III (at DESY) website

Image: Ribbon diagram of the protein structure of Plasmodium falciparum Lipocalin PfLCN that comes in tertramers, i.e. complexes of four identical molecules. Fluorescence micrographs of the parasite (upper right and lower left) show that the lipocalin accumulates in vacuoles.

Credit: BNITM/EMBL, Paul-Christian Burda/Thomas Crosskey [Source]

Protecting chickens from heart disease

Protecting chickens from heart disease

The health and welfare of broiler chickens may improve thanks to University of Saskatchewan (USask) researcher Andrew Olkowski and colleagues.

More chickens are raised worldwide than any other livestock animal, so improving their health outcomes would have a big impact.

The broiler chickens that are raised for meat were genetically selected to grow extremely fast, but they often suffer from heart diseases. Heart pump failure is a major health and welfare issue for the broiler chicken industry worldwide. Globally, economic losses associated with heart failure problems in broiler chickens amount to more than $1 billion annually.  

To understand why fast-growing broiler chickens suffer from heart problems, Olkowski and collaborators compared them with their slower-growing broiler counterparts, which have a much lower risk of heart failure, and with Leghorn chickens, which are resistant to heart failure.

Read more on the Canadian Light Source website

Image: University of Saskatchewan researcher Andrew Olkowski. 

Cell membrane proteins imaged in 3-D

Cell membrane proteins imaged in 3-D

Scientists used lanthanide-binding tags to image proteins at the level of a cell membrane, opening new doors for studies on health and medicine.

A team of scientists including researchers at the National Synchrotron Light Source II (NSLS-II)—a U.S. Department of Energy (DOE) Office of Science User Facility at DOE’s Brookhaven National Laboratory—have demonstrated a new technique for imaging proteins in 3-D with nanoscale resolution. Their work, published in the Journal of the American Chemical Society, enables researchers to identify the precise location of proteins within individual cells, reaching the resolution of the cell membrane and the smallest subcellular organelles.
“In the structural biology world, scientists use techniques like x-ray crystallography and cryo-electron microscopy to learn about the precise structure of proteins and infer their functions, but we don’t learn where they function in a cell,” said corresponding author and NSLS-II scientist Lisa Miller. “If you’re studying a particular disease, you need to know if a protein is functioning in the wrong place or not at all.”
The new technique developed by Miller and her colleagues is similar in style to traditional methods of fluorescence microscopy in biology, in which a molecule called green fluorescent protein (GFP) can be attached to other proteins to reveal their location. When GFP is exposed to UV or visible light, it fluoresces a bright green color, illuminating an otherwise “invisible” protein in the cell.

>Read more on the National Synchrotron Light Source II (NSLS-II) website

Image: Ultrabright x-rays revealed the concentration of erbium (yellow) and zinc (red) in a single E.coli cell expressing a lanthanide-binding tag and incubated with erbium.

Researchers use CHESS to map protein motion

Researchers use CHESS to map protein motion

Cornell structural biologists took a new approach to using a classic method of X-ray analysis to capture something the conventional method had never accounted for: the collective motion of proteins.

And they did so by creating software to painstakingly stitch together the scraps of data that are usually disregarded in the process.
Cornell structural biologists took a new approach to using a classic method of X-ray analysis to capture something the conventional method had never accounted for: the collective motion of proteins. And they did so by creating software to painstakingly stitch together the scraps of data that are usually disregarded in the process.
Their paper, “Diffuse X-ray Scattering from Correlated Motions in a Protein Crystal,”published March 9 in Nature Communications.
As a structural biologist, Nozomi Ando, M.S. ’04, Ph.D. ’08, assistant professor of chemistry and chemical biology, is interested in charting the motion of proteins, and their internal parts, to better understand protein function. This type of movement is well known but has been difficult to document because the standard technique for imaging proteins is X-ray crystallography, which produces essentially static snapshots.

>Read more on the CHESS website
>Read also: Diffuse X-ray Scattering from Correlated Motions in a Protein Crystal

Image: This slice through the three-dimensional diffuse map shows intense peaks resulting from lattice vibration, as well as cloudy features caused by internal protein motions.

ALS reveals vulnerability in cancer-causing protein

ALS reveals vulnerability in cancer-causing protein

A promising anticancer drug, AMG 510, was developed by Amgen with the help of novel structural insights gained from protein structures solved at the Advanced Light Source (ALS).

Mutations in a signaling protein, KRAS, are known to drive many human cancers. One specific KRAS mutation, KRAS(G12C), accounts for approximately 13% of non-small cell lung cancers, 3% to 5% of colorectal cancers, and 1% to 2% of numerous other solid tumors. Approximately 30,000 patients are diagnosed each year in the United States with KRAS(G12C)-driven cancers.

Despite their cancer-triggering significance, KRAS proteins have for decades resisted attempts to target their activity, leading many to regard these proteins as “undruggable.” Recently, however, a team led by researchers from Amgen identified a small molecule capable of inhibiting the activity of KRAS(G12C) and driving anti-tumor immunity. Protein crystallography studies at the ALS provided crucial information about the structural interactions between the potential drug molecule and KRAS(G12C).

>Read more on the Advanced Light Source website

Image: A structural map of KRAS(G12C), showing the AMG 510 molecule in the binding pocket. The yellow region depicts where AMG 510 covalently attaches to the KRAS protein.
Credit: Amgen